Version 13.0.1 was released on 22 February 2025. The patch resolved a minor bug with transcript processing.

Version 13.0.0 of VarSome and VarSome Clinical was released on 22 February 2025.

Summary of Key New Features

• Lift-over of hg19 variants to hg38
• FLT3 ITD detection
• Somatic classifier improvements
• Structural variant annotation from VCF
• Improved mitochondrial variant calling
• Clinical Report improvements
• Integration of OncoKB

New Features

Lift-over of hg19 variants to hg38

Many VarSome Clinical users are changing to the hg38 reference genome. To support this shift, we now allow for variants analysed with hg19 to be referenced in analyses that are analyzed with hg38. This feature is available on demand. Please contact Support to enable.

FLT3 ITD detection

VarSome Clinical’s secondary pipeline has been updated with the integration of ITDetect. This now supports detection of FLT3 internal tandem duplications (ITDs). Annotation and somatic classification have been updated to support interpretation of ITDs.

Somatic classifier improvements

To more closely align with AMP guidelines, the following updates have been made to the somatic classifier:

• Increased reliance on curated clinical data sources
• Reduced influence of germline classifications
• Expand classification tiers to include diagnostic and prognostic evidence (including OncoKB)

These improvements better support a range of oncology applications, including solid tumors as well as hematological malignancies, by supplying a more accurate classification along with evidence for treatment guidance, molecular diagnosis, and prognostic risk stratification.

Structural variant annotation from VCF

VCF files containing structural variants (SVs) can now be uploaded to VarSome Clinical. SVs will be processed and displayed in the variant table, along with any associated gene information (if available). 

Through VarSome Clinical, you can now view the following variant types in a single environment:

• Structural variants
• Single nucleotide variants
• Small indels
• Copy number variants
• Repeat expansions

This is the first of a series of features supporting SVs to be released through 2025

Improved mitochondrial variant calling

The VarSome v.12.5.0 release introduced enhanced detection of low allelic balance mitochondrial variants, for on-demand testing purposes. This is now available to all VarSome Clinical users, integrated into all germline pipelines (both single-sample and multi-sample). 

Clinical Report improvements

Users of VarSome Clinical can now customize reports with consistent branding and layout by defining their own global settings. 

Upcoming releases in 2025 will introduce additional configuration options for Clinical Reports.

OncoKB integration

OncoKB is a globally renowned precision oncology database developed and maintained by Memorial Sloan Kettering Cancer Center. Recognized by the FDA, it provides curated information about treatments, diagnosis, prognosis, and the oncogenicity assessment of cancer gene alterations. With information at both gene and variant level, OncoKB enhances the clinical decision support offered by our somatic classifier. 

OncoKB is available on:

• VarSome.com for BRAF, TP53, and ROS1
• VarSome Premium
• VarSome Clinical
• VarSome API (coming later in Q1 2025)

Additional Updates

Storage settings

A pop-up will now appear when changing storage settings on VarSome Clinical. This is an additional confirmation step to prevent unintended changes.

Terms of access pop-up

This pop-up will no longer appear every time an analysis is opened on VarSome Clinical. This was redundant as the terms of access cover the platform when accepted on account set up.

Support

We hope you find these improvements helpful. We would love to hear any feedback and suggestions you may have. Support is available as usual from support@varsome.com.

The VarSome Team.